Update question

Just fitted a D2sun/Wiikey to my Wii. All working fine but is it "safe" to allow updates to the Wii? I set up my wifi tonight and it's asking me to do an update. Is this going to affect the mod chip? I fitted the external switch supplied so I can turn it off during the update but is it going to work afterwards? I'm guessing the answer would be yes as the mod chip is on the DVD drive?